This study aimed to compare energy balance, metabolic profiles and body composition between two inbred strains of rats (F344 and Lou) submitted to a self-selecting macronutrient. During the 3 weeks of experiment, the two strains did not differ significantly for their total energy intake; males: F344 = 5875.4 +/- 171.4 kJ, Lou = 5619.2 +/- 349.4 kJ; and females: F344 = 4058.8 +/- 118.7 kJ, Lou = 3864.4+/-166.4 kJ. However, F344 rats showed a higher weight gain, and percentage of total fat tissue, together with a lower percentage of carcass weight than Lou rats regardless of sex. The percentages of each macronutrient revealed a lower preference of protein for F344 males and the opposite in females for CHO. The thermogenic activity measured in interscapular brown adipose tissue was lower in Fischer than in Lou while the reverse was observed for leptinemia and insulinemia. These results indicate that the mechanism responsible for the regulation of body composition observed in Lou rats takes place very early in life and attest the interest in this strain for studying the features of resistance to obesity.